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mins.</span></span></div></div></div><nav id="nav"><div class="inner"><div class="toggle"><div class="lines" aria-label="Toggle navigation bar"><span class="line"></span> <span class="line"></span> <span class="line"></span></div></div><ul class="menu"><li class="item title"><a href="/" rel="start">ResearchGo</a></li></ul><ul class="right"><li class="item theme"><i class="ic i-sun"></i></li><li class="item search"><i class="ic i-search"></i></li></ul></div></nav></div><div id="imgs" class="pjax"><img src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/bgs/thumb_82.webp"></div></header><div id="waves"><svg class="waves" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 24 150 28" preserveAspectRatio="none" shape-rendering="auto"><defs><path id="gentle-wave" d="M-160 44c30 0 58-18 88-18s 58 18 88 18 58-18 88-18 58 18 88 18 v44h-352z"/></defs><g class="parallax"><use xlink:href="#gentle-wave" x="48" y="0"/><use xlink:href="#gentle-wave" x="48" y="3"/><use xlink:href="#gentle-wave" x="48" y="5"/><use xlink:href="#gentle-wave" x="48" y="7"/></g></svg></div><main><div class="inner"><div id="main" class="pjax"><div class="article wrap"><div class="breadcrumb" itemscope itemtype="https://schema.org/BreadcrumbList"><i class="ic i-home"></i> <span><a href="/">Home</a></span><i class="ic i-angle-right"></i> <span class="current" itemprop="itemListElement" itemscope itemtype="https://schema.org/ListItem"><a href="/categories/Bioinformatics/" itemprop="item" rel="index" title="In 生物信息"><span itemprop="name">生物信息</span></a><meta itemprop="position" content="1"></span></div><article itemscope itemtype="http://schema.org/Article" class="post block" lang="en"><link itemprop="mainEntityOfPage" href="https://liaochenlanruo.gitee.io/post/f6c9.html"><span hidden itemprop="author" itemscope itemtype="http://schema.org/Person"><meta itemprop="image" content="/images/head.jpg"><meta itemprop="name" content="Hualin Liu"><meta itemprop="description" content="liaochenlanruo, 分享微生物生物信息学分析方法，欢迎加入QQ群交流945751012，不接受群内广告！"></span><span hidden itemprop="publisher" itemscope itemtype="http://schema.org/Organization"><meta itemprop="name" content="了尘兰若的小坑"></span><div class="body md" itemprop="articleBody"><div class="gallery" itemscope itemtype="http://schema.org/ImageGallery"><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/bgs/thumb_82.webp" itemprop="contentUrl"></div><p>该文档可以帮助读者入门 Linux 系统，掌握常用命令和多种软件安装方式。此外还简述了全基因组测序技术，希望读者可以通过此文档初步了解生物信息学。</p><span id="more"></span><h1 id="linux初识"><a class="anchor" href="#linux初识">#</a> Linux 初识</h1><h2 id="目录结构与路径"><a class="anchor" href="#目录结构与路径">#</a> 目录结构与路径</h2><h3 id="根目录"><a class="anchor" href="#根目录">#</a> 根目录</h3><p>根目录（root）是系统最顶级目录，以 “/” 表示，其他目录均为根目录的下级目录。</p><h3 id="家目录"><a class="anchor" href="#家目录">#</a> 家目录</h3><p>家目录（home）是用户的最顶级目录，以 “~/” 表示，用户所有的目录均为家目录的下级目录。</p><h3 id="绝对路径"><a class="anchor" href="#绝对路径">#</a> 绝对路径</h3><p>绝对路径指的是目录或文件的绝对位置，是从根目录开始的完整路径，如 “/home/bio/”。可通过 “pwd” 命令获取当前目录的绝对路径。</p><h3 id="相对路径"><a class="anchor" href="#相对路径">#</a> 相对路径</h3><p>相对路径不需要从根目录开始，只要指定与当前目录的相对位置即可。</p><h3 id="当前目录"><a class="anchor" href="#当前目录">#</a> 当前目录</h3><p>当前所在的路径，以 “./“表示。</p><h3 id="上级目录"><a class="anchor" href="#上级目录">#</a> 上级目录</h3><p>也称为父目录，以 “../“表示向上一级的目录，以 “../../” 表示向上两级的目录，以此类推。</p><h2 id="命名法则"><a class="anchor" href="#命名法则">#</a> 命名法则</h2><ul><li>文档与目录均以英文命名，可使用字母、数字和下划线；</li><li>文档与目录的名称不允许存在空格；</li><li>名称区分大小写。</li></ul><h2 id="终端工具"><a class="anchor" href="#终端工具">#</a> 终端工具</h2><p>终端（terminal）是运行 Linux 命令的工具，类似于 Windows 的命令行工具。Linux 各发行版均自带终端。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/Terminal.png" alt="Linux自带终端"></p><p>远程操控 Linux 服务器时，可以使用第三方的终端工具，如 PuTTy 软件。输入 IP 地址即可远程登录服务器运行命令。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/putty.png" alt="Putty"></p><p>本地计算机与服务器之间的文件传输可以通过 FTP 软件实现，如 FileZilla。输入服务器的 IP 地址、用户名、密码以及端口即可链接服务器。如果服务器采用的时 FTP 协议，则端口填写 21，若采用的是 SFTP 协议，则端口设置为 22。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/filezilla.png" alt="FileZilla"></p><h2 id="常用的命令"><a class="anchor" href="#常用的命令">#</a> 常用的命令</h2><p><strong>pwd：</strong> 获取当前位置的绝对路径</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">pwd</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/pwd.png" alt="获取当前位置的绝对路径"></p><p><strong>mkdir：</strong> 创建目录</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">mkdir</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/mkdir.png" alt="创建tools目录"></p><p><strong>ls：</strong> 查看当前目录包含的内容</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/ls1.png" alt="查看当前目录包含的内容"></p><p>查看所有的目录和文件（包含隐藏的内容）</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> -a</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsa.png" alt="查看当前目录包含的所有内容"></p><p>查看根目录所含内容</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> /</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsroot.png" alt="查看根目录所含内容"></p><p>查看家目录所含内容</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> ~/</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lshome.png" alt="查看家目录所含内容"></p><p><strong>cd：</strong> 切换路径</p><p>进入 “tools” 目录</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">cd</span> tools</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/cdtools.png" alt="进入“tools”目录"></p><p><strong>vim：</strong> 创建 / 编辑文档</p><p>以下所有操作均需在英文输入法状态下进行。首先创建一个新文档 “example.txt”，并输入内容。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">vim</span> example.txt</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/vimexample.png" alt="创建“example.txt”文档"></p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/unwritable.png" alt="此时无法输入内容"></p><p>此时无法输入内容，需要按一下字母 “i” 键切换到输入模式。当左下角出现 “--NSERT --” 字样时，可以输入文字。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/viminsert.png" alt="vim插入模式"></p><p>输入相关的内容。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/inputsth.png" alt="vim输入内容"></p><p>输入完毕时需要先按一下 “ESC” 键退出编辑模式，此时 “--NSERT --” 字样消失。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/vimesc.png" alt="退出vim编辑模式"></p><p>按住组合键 “shift + :” 切换到 vim 操作模式，此时左下角出现一个 “:”。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/vimshift.png" alt="shift + :"></p><p>输入 “wq!” 保存修改并退出。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/vimquit.png" alt="保存并退出vim"></p><p>查看创建的文件是否在于目录下。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/ls2.png" alt="查看当前目录下的文件及目录"></p><p><strong>cp：</strong> 复制目录或文件</p><p>将创建的 “example.txt” 文档复制到上一级目录下。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">cp</span> example.txt <span class="token punctuation">..</span>/</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/cpup.png" alt="向上级目录复制文件"></p><p>查看上一级目录下是否存在刚刚复制的文档。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> <span class="token punctuation">..</span>/</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsup.png" alt="查看父目录下的文件及目录"></p><p><strong>rm：</strong> 删除目录或文件</p><p>删除 tools 目录下的 “example.txt” 文档。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">rm</span> example.txt</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/rmexample.png" alt="删除tools目录下的“example.txt”文档"></p><p>查看文档是否被删除。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/ls3.png" alt="查看是否成功删除文件"></p><p><strong>mv：</strong> 移动 / 重命名</p><p>将上一级目录下的 “example.txt” 文档移动到当前目录下。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">mv</span> <span class="token punctuation">..</span>/example.txt ./</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/mv1.png" alt="移动文件"></p><p>查看文档是否移动成功。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> <span class="token punctuation">..</span>/</pre></td></tr><tr><td data-num="2"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/ls4.png" alt="查看是否成功移动文件"></p><p>将 “example.txt” 文档重命名为 “examp2.txt”。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">mv</span> example.txt examp2.txt</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/rename.png" alt="文档重命名"></p><p>查看重命名结果。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsrename.png" alt="查看重命名结果"></p><p><strong>wget：</strong> 下载</p><p>使用 wget 工具下载基因组拼接软件 “AbySS” 到 tools 目录下。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">wget</span> http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.5/abyss-2.1.5.tar.gz</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/wgetabyss.png" alt="下载AbySS软件"></p><p><strong>tar：</strong> 压缩 / 解压缩</p><p>tar.gz 格式的文件可用 “tar zxvf” 进行解压，将刚才下载的 “abyss-2.1.5.tar.gz” 解压缩。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">tar</span> zxvf abyss-2.1.5.tar.gz</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/tar.png" alt="解压缩AbySS软件"></p><p><strong>top：</strong> 查看系统进程</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">top</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/top.png" alt="通过top查看系统进程"></p><p>按字母键 “q” 退出。Ubuntu 还带有另一个更加直观的查看系统进程的工具 “htop”。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">htop</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/htop.png" alt="通过htop查看系统进程"></p><h2 id="环境变量"><a class="anchor" href="#环境变量">#</a> 环境变量</h2><p>在软件安装的时候经常需要设置环境变量，所谓的环境变量就是告诉计算机软件的安装位置。存放环境变量的文件在用户的家目录下，为隐藏文件，可通过 “ls -a” 命令查看。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">ls</span> -a ~/</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsahome.png" alt="查看家目录中的所有文档和目录"></p><p>“.bashrc” 和 “.profile” 均为环境变量配置文件，通常我们只需要编辑 “.bashrc”。</p><h2 id="软件安装"><a class="anchor" href="#软件安装">#</a> 软件安装</h2><h3 id="源码编译安装"><a class="anchor" href="#源码编译安装">#</a> 源码编译安装</h3><p>源码安装适合于所有的 Linux 发行版以及 macOS。以刚下载的 “AbySS” 基因组拼接软件为例演示源码编译安装，一共分三步：配置（./configure）、编译（make）和安装（sudo make install）。首先进入 “AbySS” 软件目录下，并查看目录中的文件，找到配置文件 “configure”，根据 “<span class="exturl" data-url="aHR0cDovL1JFQURNRS5tZA==">README.md</span>” 中的指示对软件进行配置。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">cd</span> abyss-2.1.5/</pre></td></tr><tr><td data-num="2"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsabyss.png" alt="进入AbySS目录并查看其所含内容"></p><p>“./configure” 表示运行 configure 进行安装前配置。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ ./configure</pre></td></tr></table></figure><p>进行编译</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">make</span></pre></td></tr></table></figure><p>进行安装，需要 “sudo” 命令提供对系统目录的写入权限。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">sudo</span> <span class="token function">make</span> <span class="token function">install</span></pre></td></tr></table></figure><p><strong>注意：</strong> 以上只演示了一般的安装方法，但是 “AbySS” 软件依赖其他的一些软件，需要先安装依赖包，最后安装 “AbySS”，否则会安装失败。</p><h2 id="通过包管理工具安装"><a class="anchor" href="#通过包管理工具安装">#</a> 通过包管理工具安装</h2><p>不同的 Linux 发行版具有各自的软件包管理器。目前常用的 Linux 发行版主要是基于 “RedHat” 和 “Debian” 而制作的。<br>RedHat 系列的包管理器为 “yum”，使用方法为在终端输入 “sudo yum install -y 软件名称”。</p><p>Debian 系列的包管理器为 “apt-get”，使用方法为在终端输入 “sudo apt-get install 软件名称”。</p><p>示例：通过 apt-get 在 Ubuntu 中安装 AbySS 软件，输入命令和密码后，根据提示输入 “Y” 并按回车键进行自动安装。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">sudo</span> <span class="token function">apt-get</span> <span class="token function">install</span> abyss</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/aptabyss1.png" alt="通过apt-get安装AbySS"></p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/aptabyss2.png" alt="通过apt-get安装AbySS"></p><h2 id="添加环境变量"><a class="anchor" href="#添加环境变量">#</a> 添加环境变量</h2><p>以原核生物基因预测软件 “Prodigal” 为例演示。首先在 Github 上找到 prodigal 的源码，点击 “Clone or download”，并按照图示点击链接右侧的图标以复制 git 地址。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/githubprodigal.png" alt="复制prodigal链接"></p><p>在终端中进入 tools 目录，并输入克隆命令将项目克隆到本地计算机。命令公式为 “git clone link”。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">git</span> clone https://github.com/hyattpd/Prodigal.git</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/cloneprodigal.png" alt="克隆prodigal"></p><p>克隆完成后进入 “Prodigal” 目录。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">cd</span> Prodigal</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/cdprodigal.png" alt="进入Prodigal目录"></p><p>编译软件</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">make</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/makeprodigal.png" alt="编译prodigal"></p><p>报错信息提示找不到 gcc 命令，因此需要首先安装 gcc，输入命令后根据提示输入密码，直至安装完成。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">sudo</span> <span class="token function">apt-get</span> <span class="token function">install</span> gcc</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/installgcc.png" alt="安装gcc"></p><p>重新编译 prodigal</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">make</span></pre></td></tr><tr><td data-num="2"></td><td><pre>$ <span class="token function">ls</span></pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/lsprodigal.png" alt="查看prodigal编译结果"></p><p>编译完成后得到了可执行程序，但是系统无法找到 prodigal 的路径，因此需要我们将其所在的路径加入到环境变量中。通过 vim 打开环境变量配置文件 “.bashrc”，进入编辑模式。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">vim</span> ~/.bashrc</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/vimbashrc.png" alt="打开环境变量文件"></p><p>在文档末尾添加配置语句 <strong>“export PATH=<span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>P</mi><mi>A</mi><mi>T</mi><mi>H</mi><mo>:</mo></mrow><annotation encoding="application/x-tex">PATH:</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:.68333em;vertical-align:0"></span><span class="mord mathnormal" style="margin-right:.13889em">P</span><span class="mord mathnormal">A</span><span class="mord mathnormal" style="margin-right:.13889em">T</span><span class="mord mathnormal" style="margin-right:.08125em">H</span><span class="mspace" style="margin-right:.2777777777777778em"></span><span class="mrel">:</span></span></span></span>HOME/tools/Prodigal”</strong> 。$HOME 代表家目录，“$HOME/tools/Prodigal” 代表 prodigal 可执行程序所在的目录。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/prodigalpath.png" alt="在环境变量中添加prodigal路径"></p><p>编辑完成后保存并退出。然后执行 “source ~/.bashrc” 命令刷新，通知系统 “.bashrc” 文档已经更改。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">source</span> ~/.bashrc</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/sourcebashrc.png" alt="刷新环境变量"></p><p>测试配置是否成功。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ prodigal -h</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/prodigalhelp.png" alt="查看prodigal帮助信息"></p><p>若要将其他软件加入到环境变量，只需在后面加入其他软件所在路径即可，各软件的路径间以英文 “:“分割，不得有空格。下图为将多个软件加入到环境变量的示例。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/multiplepath.png" alt="添加多个软件路径"></p><h2 id="创建软链接"><a class="anchor" href="#创建软链接">#</a> 创建软链接</h2><p>软链接（Soft Link）相当于 Windows 系统中的快捷方式，可以将可执行程序的软链接存放至系统默认的环境变量之中，如 “/usr/bin/” 或 “/usr/local/bin” 之中。仍旧以刚编译好的 prodigal 软件为例，创建软链接的公式为 <strong>“sudo ln -s /home/bio/tools/Prodigal/prodigal /usr/local/bin/prodigal”</strong> ，根据提示输入密码完成创建。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">sudo</span> <span class="token function">ln</span> -s /home/bio/tools/Prodigal/prodigal /usr/local/bin/prodigal</pre></td></tr></table></figure><p>通过 “whereis” 命令查看软链接是否创建成功。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">whereis</span> prodigal</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/whereisprodigal.png" alt="查看prodigal安装路径"></p><p><strong>注意：</strong> 创建软链接时要输入绝对路径，否则会报错 “Too many levels of symbolic links”。</p><h2 id="通过anaconda包管理器进行安装"><a class="anchor" href="#通过anaconda包管理器进行安装">#</a> 通过 Anaconda 包管理器进行安装</h2><p><span class="exturl" data-url="aHR0cHM6Ly93d3cuYW5hY29uZGEuY29tLw==">Anaconda</span> 是一款比较易用的跨平台软件包管理器，<span class="exturl" data-url="aHR0cDovL2Jpb2NvbmRhLmdpdGh1Yi5pby8=">Bioconda</span> 是 conda 的一个通道，专门管理生物信息学软件。通过 conda 安装软件时可以一键安装所有的依赖包，大大节约了时间并降低了安装难度。Bioconda 目前有超过 600 个贡献者和 500 个成员，大部分生物信息学软件都被包含其中。用户可以到其官网搜索需要的软件是否被囊括其中。</p><p><strong>（1）安装 conda</strong></p><p>此处，我们安装 Miniconda，进入<span class="exturl" data-url="aHR0cHM6Ly9kb2NzLmNvbmRhLmlvL2VuL2xhdGVzdC9taW5pY29uZGEuaHRtbA==">官网</span>，选择适应自身系统及 python 版本的安装文件。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/Minicondapackages.png" alt="查看Miniconda安装包"></p><p>查看系统 python 版本</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ python -v</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/pythonv.png" alt="查看python版本"></p><p>可以看出该系统已经安装了 python3，因此下载 Linux Python 3.7 64-bit (bash installer)。右键单击相应安装包获取链接，使用 wget 下载至 tools 目录下。建议用户安装 Python 3，因为 Python 软件基金会将于 2020 年元旦停止对 Python 2 的维护（<span class="exturl" data-url="aHR0cHM6Ly9weXRob25jbG9jay5vcmcvJUVGJUJDJTg5JUUzJTgwJTgy">https://pythonclock.org/）。</span></p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">wget</span> https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/DownloadMiniconda.png" alt="下载Miniconda"></p><p>开始安装 Miniconda</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">bash</span> Miniconda3-latest-Linux-x86_64.sh</pre></td></tr></table></figure><p>根据提示按 “Enter” 键查看 license，并输入 “yes” 按 “Enter” 继续，按 “Enter” 确认安装位置，miniconda 被安装到家目录下的 miniconda3 目录中。最后输入 “yes”，按 “Enter” 进行初始化。最后，通过 “source ~/.bashrc” 命令刷新。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/initialMiniconda.png" alt="初始化Miniconda"></p><p><strong>（2）设置 bioconda channel</strong></p><p>在终端中输入以下三条命令添加 channels：</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ conda config --add channels defaults</pre></td></tr><tr><td data-num="2"></td><td><pre>$ conda config --add channels bioconda</pre></td></tr><tr><td data-num="3"></td><td><pre>$ conda config --add channels conda-forge</pre></td></tr></table></figure><p>至此，bioconda 配置完毕，可以通过 conda 安装生物信息学软件。下面通过 conda 安装 mapping 软件 “bwa”。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ conda <span class="token function">install</span> bwa</pre></td></tr></table></figure><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/installbwa.png" alt="安装bwa"></p><p>根据提示输入 “y” 完成安装。</p><h2 id="macos相关操作"><a class="anchor" href="#macos相关操作">#</a> MacOS 相关操作</h2><p>MacOS 与 Linux 系统相似，基本命令相同，但是软件安装存在一些差异。</p><h3 id="macos安装生物信息学软件"><a class="anchor" href="#macos安装生物信息学软件">#</a> MacOS 安装生物信息学软件</h3><h3 id="源码安装"><a class="anchor" href="#源码安装">#</a> 源码安装</h3><p>源码安装方式与 Linux 安装方式一致。</p><h3 id="创建软链接-2"><a class="anchor" href="#创建软链接-2">#</a> 创建软链接</h3><p>配置方法与 Linux 一致。</p><h3 id="环境变量-2"><a class="anchor" href="#环境变量-2">#</a> 环境变量</h3><p>MacOS 环境变量配置方法与 Linux 配置方法一致，但配置文件为家目录下的 “.bash_profile”，即运行如下命令进行编辑。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">vim</span> ~/.bash_profile</pre></td></tr></table></figure><p>编辑完成并保存后需要运行 source 命令。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token builtin class-name">source</span> ~/.bash_profile</pre></td></tr></table></figure><h3 id="包管理器"><a class="anchor" href="#包管理器">#</a> 包管理器</h3><p>MacOS 的软件包管理器为 Homebrew，可以在终端中通过以下命令安装 Homebrew。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ ruby -e <span class="token string">"<span class="token variable"><span class="token variable">$(</span><span class="token function">curl</span> -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install<span class="token variable">)</span></span>"</span></pre></td></tr></table></figure><p>通过 Homebrew 安装 mapping 软件 “bwa”。</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ brew <span class="token function">install</span> bwa</pre></td></tr></table></figure><h3 id="macos配置anaconda"><a class="anchor" href="#macos配置anaconda">#</a> MacOS 配置 Anaconda</h3><p>安装 Miniconda</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ <span class="token function">wget</span> https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh</pre></td></tr><tr><td data-num="2"></td><td><pre>$ <span class="token function">sh</span> Miniconda3-latest-MacOSX-x86_64.sh</pre></td></tr></table></figure><p>添加 Bioconda 通道</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ conda config --add channels defaults</pre></td></tr><tr><td data-num="2"></td><td><pre>$ conda config --add channels bioconda</pre></td></tr><tr><td data-num="3"></td><td><pre>$ conda config --add channels conda-forge</pre></td></tr></table></figure><p>安装软件 bwa</p><figure class="highlight bash"><figcaption data-lang="bash"></figcaption><table><tr><td data-num="1"></td><td><pre>$ conda <span class="token function">install</span> bwa</pre></td></tr></table></figure><h1 id="现代测序技术"><a class="anchor" href="#现代测序技术">#</a> 现代测序技术</h1><h2 id="二代测序next-generation-sequencing-technology"><a class="anchor" href="#二代测序next-generation-sequencing-technology">#</a> 二代测序 (&quot;Next-generation&quot; sequencing technology)</h2><p>第二代测序技术的核心思想是边合成边测序（Sequencing by Synthesis），即通过捕捉新合成的末端的标记来确定 DNA 的序列。应用最广的技术平台主要为 Illumina 公司的产品。其优点为高通量、错误率低、成本低等。</p><ul><li>Illumina 测序中的几个名词</li><li><strong>Read length：</strong> 测序的 DNA 片段的碱基长度。</li><li><strong>Insert size：</strong> 双端测序时接头（adapter）中间序列的长度。</li><li><strong>Junction：</strong> insert 序列中间未被测序的部分。</li><li><strong>Flowcell：</strong> 是指 Illumina 测序时，测序反应发生的位置，1 个 flowcell 含有 8 条 lane。</li><li><strong>Lane：</strong> 每一个 flowcell 上都有 8 条泳道，用于测序反应，可以添加试剂，洗脱等等。</li><li><strong>Raw data：</strong> 测序完成后未去接头、引物以及去除低质量序列的数据。</li><li><strong>Clean data：</strong> 去除 Raw data 中的接头序列、linker、低质量 reads、长度较短的 reads 及核糖体 RNA 和 ncRNA 产生的 reads。</li><li><strong>数据量：</strong> read 长度乘以 reads 数目。</li></ul><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/nextseqs.png" alt="二代测序名词示意图"></p><h2 id="三代测序"><a class="anchor" href="#三代测序">#</a> 三代测序</h2><p>三代测序又称为单分子测序，测序过程无需进行 PCR 扩增，可以产生超长的 reads，因此能够跨越高 GC 含量区域和高度重复区域。目前常用的测序平台包括 Pacific Biosciences（PacBio）和 Oxford Nanopore。</p><p>PacBio 以 SMRT Cell 为载体进行测序反应，SMRT Cell 是一张带有纳米孔的超薄金属片。PacBio 采用边合成便测序的方式，测序反应在纳米孔中进行，一个纳米孔中固定一个 DNA 聚合酶和一条 DNA 模板。延伸反应的过程中检测 dNTP 荧光信号以确定碱基顺序。</p><p>Oxford 开发的纳米单分子测序技术属于真正的实时测序，它基于电信号来判读碱基。</p><caption>Table 1. Characteristics, strengths and weaknesses of commonly used sequencing platforms (Besser et al. 2018)</caption><table border="1"><tr><th>Platform\Instrument</th><th>Throughput (Gb)</th><th>Read length (bp)</th><th>Strength</th><th>Weakness</th></tr><tr><td><b>Sanger sequencing</b></td></tr><tr><td>ABI 3500/3730</td><td>0.0003</td><td>Up to 1 kb</td><td>Read accuracy and length</td><td>Cost and throughput</td></tr><tr><td><b>Illumina</b></td></tr><tr><td>MiniSeq</td><td>1.7–7.5</td><td>1×75 to ×150</td><td>Low initial investment</td><td>Run and read length</td></tr><tr><td>MiSeq</td><td>0.3–15</td><td>1×36 to 2×300</td><td>Read length, scalability</td><td>Run length</td></tr><tr><td>NextSeq</td><td>10–120</td><td>1×75 to 2×150</td><td>Throughput</td><td>Run and read length</td></tr><tr><td>HiSeq (2500)</td><td>10–1000</td><td>×50 to ×250</td><td>Read accuracy, throughput</td><td>High initial investment, run</td></tr><tr><td>NovaSeq 5000/6000</td><td>2000–6000</td><td>2×50 to ×150</td><td>Read accuracy, throughput</td><td>High initial investment, run</td></tr><tr><td><b>IonTorrent</b></td></tr><tr><td>PGM</td><td>0.08–2</td><td>Up to 400</td><td>Read length, speed</td><td>Throughput, homopolymers</td></tr><tr><td>S5</td><td>0.6–15</td><td>Up to 400</td><td>Read length, speed</td><td>Homopolymers</td></tr><tr><td>Proton</td><td>10–15</td><td>Up to 200</td><td>Speed, throughput</td><td>Homopolymers</td></tr><tr><td><b>Pacific BioSciences</b></td></tr><tr><td>PacBio RSII</td><td>0.5–1</td><td>Up to 60 kb</td><td>ead length, speed (Average 10 kb, N50 20 kb)</td><td>High error rate and initial</td></tr><tr><td>Sequel</td><td>5–10</td><td>Up to 60 kb</td><td>Read length, speed (Average 10 kb, N50 20 kb)</td><td>High error rate</td></tr><tr><td><b>Oxford Nanopore</b></td></tr><tr><td>MInION</td><td>0.1–1</td><td>Up to 100 kb</td><td>Read length, portability</td><td>High error rate, run length</td></tr></table><h2 id="常见序列格式"><a class="anchor" href="#常见序列格式">#</a> 常见序列格式</h2><h3 id="fastq"><a class="anchor" href="#fastq">#</a> Fastq</h3><p>我们得到的下机序列一般为 fastq 格式，每一条 read 包含 4 行，第一行为测序仪器信息以及测序信息，第二行为碱基序列，第三行一般无信息，第四行为对应第二行中每个碱基的测序质量信息。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/fastq.png" alt="fastq文件内容"></p><caption>Table 2. Descriptions of the first line of the fastq file</caption><table border="1"><tr><th>Strings</th><th>Description</th></tr><tr><td>@ST-E00310</td><td>The unique instrument name</td></tr><tr><td>147</td><td>The run id</td></tr><tr><td>HVT25CCXX</td><td>The flowcell id</td></tr><tr><td>3</td><td>Flowcell lane</td></tr><tr><td>1011</td><td>The number within the flowcell lane</td></tr><tr><td>13382</td><td>‘x’-coordinate of the cluster within the title</td></tr><tr><td>1819</td><td>‘y’-coordinate of the cluster within the title</td></tr><tr><td>1</td><td>The number of a pair, 1 or 2 (paired-end or mate-pair reads only)</td></tr><tr><td>N</td><td>Y if the read fails filter (read is bad), N otherwise</td></tr><tr><td>0</td><td>0 when none of the control bits are on, otherwise it is an even number</td></tr><tr><td>TGAAGACA</td><td>Index sequence</td></tr></table><h3 id="fasta"><a class="anchor" href="#fasta">#</a> Fasta</h3><p><span class="exturl" data-url="aHR0cDovL3NjaWtpdC1iaW8ub3JnL2RvY3MvMC41LjIvZ2VuZXJhdGVkL3NrYmlvLmlvLmZvcm1hdC5mYXN0YS5odG1sP2hpZ2hsaWdodD1mYXN0YSNtb2R1bGUtc2tiaW8uaW8uZm9ybWF0LmZhc3Rh">FASTA</span> 格式为文本文档，内含核苷酸或氨基酸序列以及其 IDs。每条序列包含两部分，第一部分为 ID 及注释信息，以 <strong>&quot;&gt;&quot;</strong> 开头，at the start, 第二部分为核苷酸序列或氨基酸序列。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/fasta.png" alt="fasta文件内容"></p><h3 id="genbank"><a class="anchor" href="#genbank">#</a> Genbank</h3><p><span class="exturl" data-url="aHR0cDovL3NjaWtpdC1iaW8ub3JnL2RvY3MvMC41LjIvZ2VuZXJhdGVkL3NrYmlvLmlvLmZvcm1hdC5nZW5iYW5rLmh0bWw=">GenBank</span> 格式包含了基因组序列和注释信息。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/Genbank.png" alt="Genbank文件内容"></p><h3 id="gff3"><a class="anchor" href="#gff3">#</a> GFF3</h3><p><span class="exturl" data-url="aHR0cDovL3NjaWtpdC1iaW8ub3JnL2RvY3MvMC41LjIvZ2VuZXJhdGVkL3NrYmlvLmlvLmZvcm1hdC5nZmYzLmh0bWw/aGlnaGxpZ2h0PWdmZiNtb2R1bGUtc2tiaW8uaW8uZm9ybWF0LmdmZjM=">GFF3</span> (Generic Feature Format version 3) 格式描述了序列的特征，每一行含有 9 列数据，列与列之间以制表符分割。</p><p><img data-src="https://fastly.jsdelivr.net/gh/liaochenlanruo/cdn@master/img/custom/pgcgap/Linux_WGS/GFF3.PNG" alt="GFF3文件内容"></p><h2 id="基因组拼接基本概念"><a class="anchor" href="#基因组拼接基本概念">#</a> 基因组拼接基本概念</h2><h3 id="测序深度"><a class="anchor" href="#测序深度">#</a> 测序深度</h3><p>测序深度（Sequencing depth）指测序得到的总碱基数（read 长度 x reads 数目）与待测基因组大小的比值。假设一个基因组大小为 2M，测序深度为 10X，那么获得的总数据量为 20M。</p><h3 id="测序覆盖度"><a class="anchor" href="#测序覆盖度">#</a> 测序覆盖度</h3><p>指测序获得的序列占整个基因组的比例。由于基因组中的高 GC、重复序列等复杂区域的存在，测序获得的序列经常无法覆盖基因组上所有的区域。例如覆盖度是 96%，表明还有 4% 的序列区域未测到。</p><h3 id="read-contig-scaffold"><a class="anchor" href="#read-contig-scaffold">#</a> Read、Contig、Scaffold</h3><p>测序得到的序列被称作 reads，在一个 read 中连续的 N 个碱基所组成的序列称作 k-mer，把 k-mer 集合拼接起来形成的长 DNA 序列称为 contig。通过 pair ends 信息将 contigs 按顺序进行排列得到 scaffold。</p><h3 id="n50"><a class="anchor" href="#n50">#</a> N50</h3><p>将 contigs 或 scaffolds 根据长度从大到小排列并累加，当其累计长度达到全部组装序列总长度的 50% 时，加上去的最后一个 contig 或 scaffold 的大小即为 N50 的大小，N50 是评价基因组拼接质量的重要参数。</p><h1 id="参考文献"><a class="anchor" href="#参考文献">#</a> 参考文献</h1><p>Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. <em>Clinical Microbiology and Infection</em>, 2018, 24: 335-341</p><div class="tags"><a href="/tags/Linux/" rel="tag"><i class="ic i-tag"></i> Linux</a> <a href="/tags/WGS/" rel="tag"><i class="ic i-tag"></i> WGS</a></div></div><footer><div class="meta"><span class="item"><span class="icon"><i class="ic i-calendar-check"></i> </span><span class="text">Edited on</span> <time title="Modified: 2022-05-31 09:41:33" itemprop="dateModified" datetime="2022-05-31T09:41:33+08:00">2022-05-31</time> </span><span id="post/f6c9.html" class="item leancloud_visitors" data-flag-title="Linux和基因组测序技术初识" title="Views"><span class="icon"><i class="ic i-eye"></i> </span><span class="text">Views</span> <span class="leancloud-visitors-count"></span> <span class="text">times</span></span></div><div class="reward"><button><i class="ic i-heartbeat"></i> Donate</button><p>Give me a cup of 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data-title="Contents"><ol class="toc"><li class="toc-item toc-level-1"><a class="toc-link" href="#linux%E5%88%9D%E8%AF%86"><span class="toc-number">1.</span> <span class="toc-text">Linux 初识</span></a><ol class="toc-child"><li class="toc-item toc-level-2"><a class="toc-link" href="#%E7%9B%AE%E5%BD%95%E7%BB%93%E6%9E%84%E4%B8%8E%E8%B7%AF%E5%BE%84"><span class="toc-number">1.1.</span> <span class="toc-text">目录结构与路径</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#%E6%A0%B9%E7%9B%AE%E5%BD%95"><span class="toc-number">1.1.1.</span> <span class="toc-text">根目录</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E5%AE%B6%E7%9B%AE%E5%BD%95"><span class="toc-number">1.1.2.</span> <span class="toc-text">家目录</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E7%BB%9D%E5%AF%B9%E8%B7%AF%E5%BE%84"><span class="toc-number">1.1.3.</span> <span class="toc-text">绝对路径</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E7%9B%B8%E5%AF%B9%E8%B7%AF%E5%BE%84"><span class="toc-number">1.1.4.</span> <span class="toc-text">相对路径</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E5%BD%93%E5%89%8D%E7%9B%AE%E5%BD%95"><span class="toc-number">1.1.5.</span> <span class="toc-text">当前目录</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E4%B8%8A%E7%BA%A7%E7%9B%AE%E5%BD%95"><span class="toc-number">1.1.6.</span> <span class="toc-text">上级目录</span></a></li></ol></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%91%BD%E5%90%8D%E6%B3%95%E5%88%99"><span class="toc-number">1.2.</span> <span class="toc-text">命名法则</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E7%BB%88%E7%AB%AF%E5%B7%A5%E5%85%B7"><span class="toc-number">1.3.</span> <span class="toc-text">终端工具</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%B8%B8%E7%94%A8%E7%9A%84%E5%91%BD%E4%BB%A4"><span class="toc-number">1.4.</span> <span class="toc-text">常用的命令</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E7%8E%AF%E5%A2%83%E5%8F%98%E9%87%8F"><span class="toc-number">1.5.</span> <span class="toc-text">环境变量</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E8%BD%AF%E4%BB%B6%E5%AE%89%E8%A3%85"><span class="toc-number">1.6.</span> <span class="toc-text">软件安装</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#%E6%BA%90%E7%A0%81%E7%BC%96%E8%AF%91%E5%AE%89%E8%A3%85"><span class="toc-number">1.6.1.</span> <span class="toc-text">源码编译安装</span></a></li></ol></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E9%80%9A%E8%BF%87%E5%8C%85%E7%AE%A1%E7%90%86%E5%B7%A5%E5%85%B7%E5%AE%89%E8%A3%85"><span class="toc-number">1.7.</span> <span class="toc-text">通过包管理工具安装</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E6%B7%BB%E5%8A%A0%E7%8E%AF%E5%A2%83%E5%8F%98%E9%87%8F"><span class="toc-number">1.8.</span> <span class="toc-text">添加环境变量</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%88%9B%E5%BB%BA%E8%BD%AF%E9%93%BE%E6%8E%A5"><span class="toc-number">1.9.</span> <span class="toc-text">创建软链接</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E9%80%9A%E8%BF%87anaconda%E5%8C%85%E7%AE%A1%E7%90%86%E5%99%A8%E8%BF%9B%E8%A1%8C%E5%AE%89%E8%A3%85"><span class="toc-number">1.10.</span> <span class="toc-text">通过 Anaconda 包管理器进行安装</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#macos%E7%9B%B8%E5%85%B3%E6%93%8D%E4%BD%9C"><span class="toc-number">1.11.</span> <span class="toc-text">MacOS 相关操作</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#macos%E5%AE%89%E8%A3%85%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E5%AD%A6%E8%BD%AF%E4%BB%B6"><span class="toc-number">1.11.1.</span> <span class="toc-text">MacOS 安装生物信息学软件</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E6%BA%90%E7%A0%81%E5%AE%89%E8%A3%85"><span class="toc-number">1.11.2.</span> <span class="toc-text">源码安装</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E5%88%9B%E5%BB%BA%E8%BD%AF%E9%93%BE%E6%8E%A5-2"><span class="toc-number">1.11.3.</span> <span class="toc-text">创建软链接</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E7%8E%AF%E5%A2%83%E5%8F%98%E9%87%8F-2"><span class="toc-number">1.11.4.</span> <span class="toc-text">环境变量</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E5%8C%85%E7%AE%A1%E7%90%86%E5%99%A8"><span class="toc-number">1.11.5.</span> <span class="toc-text">包管理器</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#macos%E9%85%8D%E7%BD%AEanaconda"><span class="toc-number">1.11.6.</span> <span class="toc-text">MacOS 配置 Anaconda</span></a></li></ol></li></ol></li><li class="toc-item toc-level-1"><a class="toc-link" href="#%E7%8E%B0%E4%BB%A3%E6%B5%8B%E5%BA%8F%E6%8A%80%E6%9C%AF"><span class="toc-number">2.</span> <span class="toc-text">现代测序技术</span></a><ol class="toc-child"><li class="toc-item toc-level-2"><a class="toc-link" href="#%E4%BA%8C%E4%BB%A3%E6%B5%8B%E5%BA%8Fnext-generation-sequencing-technology"><span class="toc-number">2.1.</span> <span class="toc-text">二代测序 (&quot;Next-generation&quot; sequencing technology)</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E4%B8%89%E4%BB%A3%E6%B5%8B%E5%BA%8F"><span class="toc-number">2.2.</span> <span class="toc-text">三代测序</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%B8%B8%E8%A7%81%E5%BA%8F%E5%88%97%E6%A0%BC%E5%BC%8F"><span class="toc-number">2.3.</span> <span class="toc-text">常见序列格式</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#fastq"><span class="toc-number">2.3.1.</span> <span class="toc-text">Fastq</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#fasta"><span class="toc-number">2.3.2.</span> <span class="toc-text">Fasta</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#genbank"><span class="toc-number">2.3.3.</span> <span class="toc-text">Genbank</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#gff3"><span class="toc-number">2.3.4.</span> <span class="toc-text">GFF3</span></a></li></ol></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%9F%BA%E5%9B%A0%E7%BB%84%E6%8B%BC%E6%8E%A5%E5%9F%BA%E6%9C%AC%E6%A6%82%E5%BF%B5"><span class="toc-number">2.4.</span> <span class="toc-text">基因组拼接基本概念</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#%E6%B5%8B%E5%BA%8F%E6%B7%B1%E5%BA%A6"><span class="toc-number">2.4.1.</span> <span class="toc-text">测序深度</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#%E6%B5%8B%E5%BA%8F%E8%A6%86%E7%9B%96%E5%BA%A6"><span class="toc-number">2.4.2.</span> <span class="toc-text">测序覆盖度</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#read-contig-scaffold"><span class="toc-number">2.4.3.</span> <span class="toc-text">Read、Contig、Scaffold</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#n50"><span class="toc-number">2.4.4.</span> <span class="toc-text">N50</span></a></li></ol></li></ol></li><li class="toc-item toc-level-1"><a class="toc-link" href="#%E5%8F%82%E8%80%83%E6%96%87%E7%8C%AE"><span class="toc-number">3.</span> <span class="toc-text">参考文献</span></a></li></ol></div><div class="related panel pjax" data-title="Related"><ul><li><a href="/post/19824.html" rel="bookmark" title="生物信息学1：VMware虚拟机及Bio-linux安装与配置">生物信息学1：VMware虚拟机及Bio-linux安装与配置</a></li><li><a href="/post/9.html" rel="bookmark" title="生物信息学2：VirtualBox虚拟机及Bio-Linux安装">生物信息学2：VirtualBox虚拟机及Bio-Linux安装</a></li><li><a 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